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After a Cardassian man arrives on the station suffering from an illness that he could only have contracted at a Bajoran labor camp during the Occupation, Major Kira leads an investigation to determine whether he is actually a notorious war criminal.

In Odo's office, Kira admits to CommanderBenjamin Sisko and Odo that the Bajoran Provisional Government has not listed the Cardassian, Aamin Marritza, for any war crimes. However, she is certain that there is no way to contract Kalla-Nohra Syndrome except for the mining accident at Gallitep. As she describes the brutal conditions at the camp, her voice cracks with emotion. Sisko decides to talk to Marritza alone.

In the brig, when Sisko asks Marritza about his illness, Marritza claims he has Pottrik Syndrome, a similar condition to Kalla-Nohra, and that his medication is the same as that which is used to treat Kalla-Nohra Syndrome. Further, he denies ever being at a labor camp, as he is a file clerk who resides on Kora II. A Bajoran prisoner in another holding cell wakes as the Cardassian speaks and yells for Odo, refusing to be held in the same room as Marritza.

Back in Sisko's office, Bashir confirms that a bio-probe proved Marritza's condition is Kalla-Nohra, not Pottrik Syndrome. His conversation with Sisko is interrupted as Kira contacts Sisko to inform him that he has an incoming transmission from the Bajoran Minister of State. Bashir exits and Sisko puts Minister Kaval on his desktop monitor's viewscreen. Kaval has contacted Sisko to congratulate and thank him for detaining Marritza. However, Sisko reminds Kaval that the Cardassian has done nothing wrong and he therefore has no reason to detain the man much longer. The minister assertively assures Sisko that the man will pay if he was indeed at Gallitep and reminds Sisko that Deep Space 9 is a Bajoran station.

Finding Kira sitting at a table in the Replimat, Sisko joins her to inform her that Odo, as Chief of Security, will take over the Marritza investigation. He acknowledges that Minister Kaval put Kira in charge, but he does not feel Kira can be entirely objective in the investigation. While Kira acknowledges that she is not objective, she promises as his first officer to handle the case fairly, as she owes it to the victims of Gallitep. Sisko reluctantly agrees and informs Odo of the change via his combadge.

Odo is releasing an intoxicated Bajoran as Kira enters the security office. The man, Kainon, tells Odo he wants to know when the Cardassian will be hanged. Once Kainon is gone, Odo informs Kira that he has done a background check and confirmed what little they know about Marritza so far.

As Kira enters the holding cell area, Marritza finishes a bowl of sem'hal stew, which he says could use some yamok sauce. Kira commences interrogating Marritza about his claim of having "missed [the] honor" of being at Gallitep, confronting him with the results of the bioscan that proved him to have been. Promising to "make [his] lies more opaque," Marritza confesses to having served at the camp as a file clerk, without any connection to the atrocities that had taken place there under GulDarhe'el – even as he minimizes them, turning Kira's interrogation into a debate over the deaths being the result of fights between the workers and industrial accidents (Marritza's story) and systematic abuse and brutality (Kira's).

Marritza tells Kira that it was Gul Darhe'el himself who began circulating rumors of large-scale massacres at Gallitep, based on the logic that the rumors on their own would be just as effective as having actually killed millions of Bajorans in achieving the Cardassians' main goal: "To keep you Bajorans thinking of yourselves as victims. To keep you afraid… and helpless."

Having revealed his relatively innocuous identity and the truth of his presence on Gallitep, he challenges Kira to release him, accusing her of being more interested in vengeance than justice.

Having learned of the detention of Aamin Marritza as a Cardassian national, Gul Dukat hails Commander Sisko via subspace, demanding Marritza's release and noting that his detention breached a Federation promise to allow free and safe passage through the station and its jurisdiction. Sisko stalls for time, telling Dukat that while he would like nothing better than to release Marritza there were still some inconsistencies in his story that needed to be cleared up. Dukat gives Sisko a thinly-veiled warning about allowing Bajoran thirst for violence to create tension between the Federation and the Cardassians. He closes the channel with the warning that the Cardassians will hold Sisko responsible should "those Bajoran hatemongers get their hands on" Marritza.

"What are you looking for?""Answers."

Meanwhile, Kira is on the Promenade, gazing out of the window. When Dax asks her what she's looking for, Kira replies "Answers." She confides in Dax that even if Marritza is just a file clerk she still wants to see him punished, and that in some way she wants him to be more than just a file clerk; to actually be something worse. As far as Kira is concerned, Marritza is guilty by virtue of simply having been on Gallitep, and that his trial and punishment would bring some "satisfaction" or closure to the Bajorans. However, Dax believes that Kira is "trying too hard to believe" what she's saying and that she already knows that punishing Marritza without reason would not serve any purpose because Kira already knows that simple vengeance is not enough. Dax walks away to leave Kira to her thoughts.

Having consulted the Bajoran Central Archives, Commander Sisko informs his senior staff that Marritza's claims are accurate: there was a filing clerk on Gallitep by the name of Aamin Marritza. A further claim, that Marritza had been teaching filing at a Cardassian military academy on Kora II, is also verified. The Archives have also sent the only known photograph of Marritza from his days at Gallitep; a very blurred image with him in the background on one side. Dax carries out an image enhancement routine which cleans up the image enough to show that the man in the brig claiming to be Aamin Marritza and the man in the picture identified as Aamin Marritza are not the same man. Examining the images of the two other Cardassians in the shot standing in profile relative to the camera, Sisko has an idea: he asks Dax to enhance one of them. The imaging program extrapolates the profile into an impression of the full face, which does match the man in the holding cell. Dax checks the photo's legend, which presents the senior staff with the revelation that the man in the photo thus identified – and thus the man in their custody – is in fact Gul Darhe'el.

Kira immediately confronts Darhe'el with this knowledge. He accepts his fate, noting that the Bajorans "can only execute me once," and proceeds to taunt Kira with his "accomplishments." Rejecting the notion of a war crimes tribunal on the grounds that there had been no war – the Bajorans having surrendered so quickly – he claims that he did everything he did to wipe out "Bajoran scum" because it needed to be done, he disavows any guilt on the part of his soldiers for having carried out the atrocities in question and derides the efforts of the Bajoran resistance to liberate their homeworld, dismissing Kira's cell in particular as a mere annoyance. Kira coldly challenges him to include his revelations in his testimony to the tribunal, knowing full well that they will sentence him to death, and he replies:

"Let them. Don't you see; it doesn't change anything! Kill me. Torture me… it doesn't matter. You've already lost, Major. You can never undo what I've accomplished. The dead will still be dead!"

Shaken to the core, Kira is given a glass of Maraltian Seev-ale by Odo, who suggests that she go and lie down after the shock of the revelations she has just been forced to hear. She refuses to do so: that would be what Darhe'el would want, to send a Bajoran scurrying off to hide in a corner. She goes on to tell Odo what Darhe'el said about the Shakaar cell, leading Odo to counsel her to not to reveal that kind of personal information – but Kira hadn't revealed her membership of Shakaar to Darhe'el during the interrogation.

This sets Odo thinking: as important as Darhe'el was in the Cardassian occupational leadership, he wouldn't necessarily have known that Kira was a member of the Shakaar cell. Had he been in charge of putting down the resistance then he probably would have known, but he was in charge of a labor camp – why would he have had that information? Realizing that something doesn't fit, Kira goes back to interrogate Darhe'el again, while Odo tells the computer to review all off-station requests for information about Major Kira within the previous eight months.

Back in the holding area, Kira demands to know how Darhe'el knew of her membership in Shakaar. Darhe'el reminds her of his earlier remarks concerning Marritza's filing system and how efficient it was, claiming to remember her name from an action report having previously forgotten about it until he was reminded of it on his arrival on the station. He then challenges Kira to answer some questions of his own – unless Kira is afraid to do so.

Meanwhile, outside the security office, a group of Bajorans has gathered. Wearing the "dust-wraps" around their face that prevented Bajoran laborers from being suffocated in the mines, they are survivors of Gallitep and Gul Darhe'el's brutality, holding a vigil.

Passing them (and Quark) on the way, Odo goes to the infirmary to consult with Bashir: three months previously there was a request for information on Major Kira from Kora II, by Aamin Marritza. Odo asks Bashir to look into Marritza's medical records. At this point, Dax informs Odo from Ops that Gul Dukat is responding to his subspace hail and his request for access to the Cardassian government's files on Gul Darhe'el. After reminiscing for a moment, Dukat declines Odo access to the files, but notes that they would only tell Odo what Dukat himself is telling him: Gul Darhe'el is dead, that he is buried underneath one of Cardassia's largest military monuments, and that Dukat himself attended his funeral.

Odo tells Dukat that the man in his custody has admitted to being Darhe'el, shocking and enraging Dukat. He accuses Odo of a plot to discredit the Cardassians, and Odo suggests that access to Darhe'el's files would prove Dukat's case. Dukat relents, and gives Odo limited access to the files.

In the brig, the prisoner whom Kira still believes to be Darhe'el asks her how many Cardassians she killed. Kira claims not to have kept count, but the prisoner suggests that she did and that she also targeted Cardassian civilians on Bajor, noting that 'one of the most effective terrorist weapons was random violence." Kira admits to regretting some of the things she did during the Occupation, but insists that she had no choice: Bajor was fighting for its survival. The prisoner claims that the Cardassians were doing the same: they had an empire to manage and protect, and had urgent need of Bajoran resources. He finishes on the note "What you call genocide, I called a day's work!" At this point, Odo arrives and asks to speak to Kira outside. He tells her that, based on the research he and Dr Bashir have carried out, the man in the cell apparently wanted to be caught.

In the commander's office Kira, Odo, and Commander Sisko assemble the evidence at hand. Odo shows Sisko a death certificate for Darhe'el included among the files which Dukat gave Odo access to, that lists him as having died six years previously from a massive coleibric hemorrhage. Kira denounces the certificate as a fake, a Cardassian ruse to trick station authorities into releasing him. Odo presents further evidence supplied by Dukat showing that, on the day of the accident at Gallitep when all known cases of Kalla-Nohra Syndrome were contracted, Darhe'el was back on Cardassia being awarded the Proficient Service Medallion, and thus never actually contracted the condition suffered by the man in the cell. Odo also notes that, during the prisoner's last two weeks on Kora II, he resigned his post at the military academy, put his affairs in order – even providing handsomely for his housekeeper – and booked passage on a ship specifically scheduled to stop at Deep Space 9, returning him to Bajoran jurisdiction – an unusual choice of travel plan for a Cardassian war criminal.

Kira will hear none of it. Conceding the interesting question that the evidence raises, she insists that the prisoner will stand trial on Bajor. Sisko points out that the decision has still to be made, and Kira challenges him to speak to the prisoner for himself. At this point Dr. Bashir enters with additional medical evidence: aside from his receiving treatment for Kalla-Nohra, the prisoner's medical history is consistent with his relatively advanced years, with one exception. Five years previously he began taking large doses of a dermatiraelian plastiscine: a dermal regenerative agent used to maintain skin resilience after large-scale cosmetic surgery. Kira is unable to deny the obvious conclusion of all the evidence, that the man in the cell is not Darhe'el but someone who has been surgically altered to resemble him.

Kira returns to the brig to confront the prisoner. She asks the prisoner how he came to contract Kalla-Nohra Syndrome when his own progress reports showed him to be on Cardassia at the time receiving the Proficient Service Medallion. The prisoner denounces the reports as inaccurate, but Kira asks him why he is taking a dermal regenerative, and even begins to fill out the gaps. Increasingly frantic in his Darhe'el role, he demands that Kira leave and yells for security to escort her out.

He begins detailing how he ordered his guards to slaughter the laborers on Gallitep while "the useless office clerks were busy packing their precious files" and this prompts Kira to ask why, if that was his opinion of them did he take Marritza's name. The prisoner continues to ignore Kira's questions, proceeding to rant and rave over Bajor and the Bajorans. As she listens to him, Kira's demeanor changes, and she tells him straight: he is Marritza.

"That's not true! I'm alive! I will always be alive! It's Marritza who's dead! (laughing) Marritza, who was good for nothing but cowering under his bunk and weeping like a woman! Who would every night, cover his ears, because he couldn't bear to hear the screaming for mercy of the Bajorans! He would only…"

With that, Aamin Marritza breaks down and sinks onto his bunk, weeping uncontrollably.

"I covered my ears every night, but… I couldn't bear to hear those horrible screams. You have no idea what it's like to be a coward. To see these horrors, and do nothing. Marritza's dead. He deserves to be dead."

Now sympathetic, Kira moves to release him: "You didn't commit those crimes and you couldn't stop them, you were only one man." But Marritza begs her not to reveal his identity, insisting that he go to trial as Darhe'el so that he can be "punished" – that all of his people must be punished for what they did to the Bajorans. When she asks him why he's doing this, Marritza replies:

"For Cardassia. Cardassia will only survive if it stands before Bajor and admits the truth. My trial will force Cardassia to admit its guilt… And we're guilty, all of us. …My death is necessary!"

Kira, now emotional herself, replies "What you're asking for is another murder… Enough good people have already died … I won't help kill another."

Kira holding Marritza's dead body

A little later, Kira and Odo walk Marritza along the Promenade to a ship that will take him back home to Kora II. Marritza says there is nothing for him to go back to, but Kira promises that the authorities will help him get back on his feet. Marritza is bitter at Kira: as Gul Darhe'el, his trial might have helped bring about a new Cardassia; as a lowly filing clerk, he can do nothing. But Kira says that, if Cardassia is to change, it will need men of honor like Marritza to help it.

Suddenly Kainon reappears from out of the crowd and stabs Marritza in the back, wounding him fatally. Odo apprehends him before Marritza even hits the floor, and a distraught Kira demands of Kainon:

"Why? He wasn't Darhe'el! WHY?" Kainon's sneered reply is that "He's a Cardassian. That's reason enough." Marritza is already dead as Kira replies, as much to herself as to anyone else, "No. It's not."

"Kill me! Torture me! It doesn't matter! You've already lost, major! You can never undo what I've accomplished. The dead will still be dead!"

- Marritza/Darhe'el, taunting Kira

"Commander, if you'd been there twelve years ago when we liberated that camp… if you'd seen the things I saw… all those Bajoran bodies, starved, brutalized. You know what Cardassian policy was? Oh, I'm not even talking about the murder, murder was just the end of the fun for them; first came the humiliation! Mothers raped in front of their children, husbands beaten until their wives couldn't recognize them, old people buried alive because they couldn't work anymore!"

- Kira, to Sisko and Odo

"If your lies are going to be this transparent, it's going to be a very short interrogation."
"Well, in that case, I'll try to make my lies more opaque."

- Kira and Marritza/Darhe'el

"What was your rank at Gallitep, what were your duties?"
"You don't want to know."
"Just answer the question."
"You'll be disappointed…"
"I'll risk it."
"I had the distinction of serving in the exalted position of filing clerk."
"Filing clerk?"
"I told you you'd be disappointed. Actually I would have preferred to avoid military service altogether, but I had the good fortune to be posted to the records office at Gallitep, and I turned out to be an exemplary file clerk. In fourteen units of service, I never misplaced or lost a record. I received numerous commendations. Gul Darhe'el himself called my computer filing system 'a masterpiece of meticulous exactitude'. Well, there you are. My secret's out, my crimes laid bare… I await execution."

- Kira and Marritza/Darhe'el

"You saw what we wanted you to see. Who do you think started the rumors about brutality at Gallitep? It was Gul Darhe'el himself. Now there was a leader. A brilliant, extraordinary man. He knew that to rule by fear was to rule completely. Why bother with actual mass murder, when the mere reports of such incidents achieved the same effect?"

- Marritza/Darhe'el

"This Bajoran obsession with alleged Cardassian improprieties during the occupation is really quite distasteful."
"I suppose if you're Bajoran, so was the occupation."

- Dukat and Sisko

"What did you do? Did you kill the real Marritza so you could take his place? Well, you'll pay for that death, and all the others you're responsible for."
(chuckles) "Oh, I don't think I could pay for all of them, major, there were so many. And you can only execute me once."

- Kira and Marritza/Darhe'el

"What lies? You mean my failure to divulge my true identity? Believe me major, I yearned to tell you. But I knew how much more satisfaction you would have if you found out for yourself, and that was my only deception. Marritza was a magnificent file clerk. And I, Gul Darhe'el? I hope you'll not think it immodest of me to say so, but I was a magnificent leader. Oh, you never saw Gallitep at its height. For a labor camp, it was the very model of order and efficiency. And why? For that, you have to look to the top. To me! My word, my every glance, was law. And my verdict was always the same: Guilty."
"You're insane!"
"Oh, no, no, major… you can't dismiss me that easily. I did what had to be done. My men understood that, and that's why they loved me. I would order them to go out and kill Bajoran scum, and they'd do it, they'd murder them! They'd come back covered in blood but they felt clean! Now why did they feel that way, major? Because they were clean!"

- Marritza/Darhe'el and Kira

"I do miss working with you, Odo. I miss our games of Kalevian montar."
"As I recall, Gul Dukat, we played one game, and you cheated."
(laughs) "The same old Odo. Like a blunt instrument."

"You're Marritza, aren't you?"
"You mistake me for that bug? That whimpering nothing? Oh, you stupid Bajoran girl. Don't you know who I am? I'm your nemesis. I'm your nightmare. I'm the Butcher of Gallitep."
"The Butcher of Gallitep died six years ago. You're Aamin Marritza, his filing clerk."
"That's not true. I am alive. I will always be alive! It's Marriza who is dead. Marritza, who was good for nothing but cowering under his bunk and weeping like a woman. Who, every night, covered his ears because he couldn't bear to hear the screaming… for mercy… of the Bajorans…"

-Kira and Marritza/Darhe'el

"You have no idea what it's like to be a coward. To see these horrors and do nothing."

The original pitch for this episode, by Lisa Rich and Jeanne Carrigan-Fauci was based upon the simple conflict inherent in the idea of someone having to defend their worst enemy. Carrigan-Fauci explains that "the basic premise was 'What would happen if you had to defend your worst enemy? What would you do if you had to be responsible for his life?' There's so much inherent conflict in that concept. And, of course, it was only natural to use Kira and a Cardassian in that situation and to have them both learn something about each other." (Star Trek: Deep Space Nine Companion)

This episode introduces the character of Neela, who went on to play a crucial role in the following episode, "In the Hands of the Prophets", although she was supposed to be introduced in "The Forsaken". The producers' intention was for the audience to assume she was simply a new recurring character, thus creating an unexpected twist when she turns out to be an assassin, and they felt that seeing her twice before the final episode would accomplish this goal. However, the actress cast as Anara for "The Forsaken" "didn't work out," and she was written out of that episode. She was never supposed to be in "Dramatis Personae", so in the end, she only appeared in one episode prior to being made into a villain. (Star Trek: Deep Space Nine Companion)

Visitor agreed: "The action comes out of big issues on this show. There's action and intrigue, but the writing really lets us deal with issues we're not embarrassed to commit ourselves to as actors and people. On a sitcom, very often it's 'Should I let Johnny stay out after midnight or not?' It's an important issue, but not quite so much as Holocaust victims and facing evil in one person and how you deal with that, which is one thing I had to deal with in 'Duet.' It was kind of harrowing to have to deal with that subject matter every day, but the harder it is, the more rewarding it is." (Captains' Logs Supplemental - The Unauthorized Guide to the New Trek Voyages)

Other fans of this episode include Terry J. Erdmann, Dave Rossi, and Ira Behr, who said of it in 1999, "I thought that show was gangbusters. It was very powerful, and it still works today. It's a wonderful episode." (Crew Dossier: Kira Nerys, DS9 Season 1 DVD, Special Features)

In Captains' Logs Supplemental, Behr elaborated, "I'm very, very proud of this show. Not in the sense it's a show for all humanity, but that it was a fun show to work on. You had a character who was larger than life and reveling in his evilness. It was just a blast. It was a lot of fun to write, but it was the end of the season, and we were all very tired, so neither Peter nor I were very happy doing it. We work very well together, and the show could have, literally, been another half hour if they would have let us. It was just mind games on top of mind games, and we could have done that forever."

Mary Taylor wrote: "Duet" from DS9's second season (sic), continued the commentary on racism begun thirty years before [by the original Star Trek series]. The lesson of 'Duet'... was that each individual should be judged on his own merits and not because he is a member of a hated race". (Adventures in Time and Space)

In The New Trek Programme Guide, the authors comment that "Duet" was "the pinnacle of the season, a tightly plotted and allusive tale that could be 'about' the Simon Wiesenthal Centre, the modern Nazi's re-writing of World War Two or even Bosnia. Although the juxtaposition with the previous episode is less than ideal, with Kira seeming to go behind Sisko's back to get what she wants, the strength of the script and the performances more than make up for this. Harris Yulin excels as the coward who personalised the guilt of an entire race. This powerful and absorbing drama is also very Roddenberryesque: Kira realises, just before the clever twist ending, that his being a Cardassian is not reason enough to want to kill him". (The New Trek Programme Guide, pp. 316 – 317)

This is one of only a few DS9 episodes without a subplot. (The A-story / B-story formula had been used quite extensively in the series up to this point, and was used many more times throughout the later seasons.)